Israel's Advisory Committee for Review of Applications for Employment of Foreign Nationals said it had denied Shakir's visa, based on a recommendation by the Israeli Foreign Ministry, and because HRW had "engaged in politics in the service of Palestinian propaganda, while falsely raising the banner of "human rights".
Noting that it was not a blanket ban on HRW, Israel's Foreign Ministry later backtracked on its decision, saying that it would be willing to reexamine issuing a work visa for Omar Shakir, an American of Iraqi origin named as the NGO's Israel researcher, should the organization file an appeal.
The HRW further said it had been informed by Tel Aviv that the request had been rejected because it is "not a real human rights group".
Emmanuel Nahshon, a foreign ministry spokesman, told the AFP news agency that the group was not banned, and any Israeli and Palestinian employees would still be allowed to operate in Israel, but said: "Why should we give working visas to people whose only objective is to besmirch us and to attack us?"
HRW, a well-known nonprofit, nongovernmental human rights organization made up of roughly 400 staff members around the globe, has a history of being critical of Israel's many human rights violations, labeled so according to worldwide law and conventions.
The news emerged as Israel faced criticism from the U.N. Human Rights Council in Geneva over the 18-month jail sentence handed to an Israeli soldier who shot an incapacitated Palestinian assailant in the head.
The New York-based group monitors human rights in over 90 countries, including nations throughout the Middle East and vowed to continue its work in Israel.
"This decision and the spurious rationale should worry anyone concerned about Israel's commitment to basic democratic values", commented Deputy Executive Director of Programmes at HRW, Lain Levine.
Last year, the Foreign Ministry even requested HRW intervene in a case involving Israeli victims of human rights abuses.
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"The Israeli government is hardly the only one to disagree with our well-researched findings, but efforts to stifle the messenger signal that it has no appetite for serious scrutiny of its human rights record", Levine said.
Human Rights Watch has operated in Israel for three decades, Shakir said.
"Settlement businesses unavoidably contribute to Israeli policies that dispossess and harshly discriminate against Palestinians, while profiting from Israel's theft of Palestinian land and other resources", HRW's Arvind Ganesan said at the time.
HRW said it was "disappointing that the Israeli government seems unable or unwilling to distinguish between justified criticisms of its actions and hostile political propaganda". In the past year, Human Rights Watch documented ISIS abuses including sexual violence, rape, and torture, chemical weapons attacks by Syrian government forces in Aleppo, Saudi Arabia's male guardianship system, torture in Egypt, Saudi-led coalition airstrikes in Yemen that killed civilians, and executions in Iran, among many other issues.
Israeli politicians have strongly criticized what it perceives to be left-wing NGOs operating in Israel that receive the majority of their funding from foreign governments, and has taken steps to limit their work.
The law did not specifically refer to left-wing organisations, but it is applicable to some 25 NGOs.
Israel now joins countries such as Cuba, Egypt, Syria, Sudan and Venezuela that have blocked access for HRW's staff members.
The decision marks an ominous turn after almost three decades during which Human Rights Watch staff have had regular access without impediments to Israel and the West Bank.
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